GapMind for Amino acid biosynthesis

 

Aligments for a candidate for dapF in Desulfovibrio vulgaris Miyazaki F

Align Diaminopimelate epimerase; DAP epimerase; EC 5.1.1.7; PLP-independent amino acid racemase (uncharacterized)
to candidate 8499796 DvMF_0561 diaminopimelate epimerase (RefSeq)

Query= curated2:O67693
         (279 letters)



>lcl|FitnessBrowser__Miya:8499796 DvMF_0561 diaminopimelate
           epimerase (RefSeq)
          Length = 282

 Score =  201 bits (512), Expect = 1e-56
 Identities = 125/279 (44%), Positives = 160/279 (57%), Gaps = 19/279 (6%)

Query: 5   KLQGSGNDFVVIDDRDEKLESFLKERGVSKEDFVRKVCAFHTGVGADGLILI-KNPDNPE 63
           KL G GNDFV ID+R   L         +  D+ R VC    GVGADGL+ + + P + E
Sbjct: 12  KLHGCGNDFVFIDNRALGLPV------AAMPDWARSVCRRAFGVGADGLVFLDETPKDRE 65

Query: 64  NDFKWEFFNSDGSVAEMCGNGSRCAVRFAYERGIVGNKVRFETLAGVIKAEVYENGRKVK 123
            D+ W F+N+DGS AEMCGN SRCA   A E G  G K  F T AG+I+AE        K
Sbjct: 66  GDYIWHFYNADGSRAEMCGNASRCAALLAVELGFAGPKHVFGTDAGLIRAEADVAAGMAK 125

Query: 124 VQLTPPSKPEEKTLTVD-----GEEVIGVFINTGVPHFVVPVEDVEKVNVIKLGRAIRFH 178
           V+LTPP    + TL ++     G +++  F+NTGVPH VV   D   V+V  LG A+R H
Sbjct: 126 VELTPP---RDLTLGIELDLGEGRDMVH-FVNTGVPHAVVFKRDASTVDVRTLGAALRRH 181

Query: 179 EEFQPKGTNVNFVQPVSEDTIKVRTYERGVESETLACGTGATACAIVSYLKGLVKKKPVN 238
             F P GTN NF Q +    I +RT+ERGVE ET ACGTGA A A +++  GL  +  VN
Sbjct: 182 AHFAPAGTNANFAQVIDRRNIHLRTFERGVEDETYACGTGAAAGAFIAHALGLA-ESTVN 240

Query: 239 VLTRSGEVLTIDFSEDLKEVFLTGSVYKVFEGRLSEEVL 277
           V +  GE+L I  S +   VFL+G   +VF G +  E L
Sbjct: 241 VRSSGGEILGI--SIEGGSVFLSGKAVRVFSGEMFLEGL 277


Lambda     K      H
   0.317    0.138    0.399 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 205
Number of extensions: 7
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 279
Length of database: 282
Length adjustment: 26
Effective length of query: 253
Effective length of database: 256
Effective search space:    64768
Effective search space used:    64768
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 47 (22.7 bits)

Align candidate 8499796 DvMF_0561 (diaminopimelate epimerase (RefSeq))
to HMM TIGR00652 (dapF: diaminopimelate epimerase (EC 5.1.1.7))

# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file:                  ../tmp/path.aa/TIGR00652.hmm
# target sequence database:        /tmp/gapView.30843.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00652  [M=270]
Accession:   TIGR00652
Description: DapF: diaminopimelate epimerase
Scores for complete sequences (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Sequence                         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
      5e-73  231.8   0.0    6.1e-73  231.5   0.0    1.0  1  lcl|FitnessBrowser__Miya:8499796  DvMF_0561 diaminopimelate epimer


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Miya:8499796  DvMF_0561 diaminopimelate epimerase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  231.5   0.0   6.1e-73   6.1e-73       5     269 ..      12     273 ..       9     274 .. 0.93

  Alignments for each domain:
  == domain 1  score: 231.5 bits;  conditional E-value: 6.1e-73
                         TIGR00652   5 kmhGlgNdFvlvdevdeelvkee.aelvrkvcdrhtgvgaDgvllvep..sseeadvklrifNsDGSeaemCGNgiR 78 
                                       k+hG gNdFv +d++   l+    ++ +r+vc+r +gvgaDg++++ +  +++e d+ ++++N+DGS+aemCGN++R
  lcl|FitnessBrowser__Miya:8499796  12 KLHGCGNDFVFIDNRALGLPVAAmPDWARSVCRRAFGVGADGLVFLDEtpKDREGDYIWHFYNADGSRAEMCGNASR 88 
                                       99**************77766666**********************987899************************* PP

                         TIGR00652  79 cfakfvyekglkekkelsvetlaglikveveeenkkvkvdmgepkfkkeeipltvekeeekeellalevlvvdvGnP 155
                                       c+a  ++e g +   ++++ t+agli +e   +    kv+++ p+  +  i+l+    e ++++ +     v++G+P
  lcl|FitnessBrowser__Miya:8499796  89 CAALLAVELGFAG-PKHVFGTDAGLIRAEADVAAGMAKVELTPPRDLTLGIELDL--GEGRDMVHF-----VNTGVP 157
                                       ************7.99***************99989********99999999887..333345555.....****** PP

                         TIGR00652 156 Hlvvfvedvekldleelgklleaheef.pegvNvefvevkkedeiklrvyERG.ageTlaCGtGavAsavvalklgk 230
                                       H+vvf  d +++d+ +lg++l+ h +f p+g+N +f++v ++ +i+lr++ERG ++eT aCGtGa+A a +a++lg+
  lcl|FitnessBrowser__Miya:8499796 158 HAVVFKRDASTVDVRTLGAALRRHAHFaPAGTNANFAQVIDRRNIHLRTFERGvEDETYACGTGAAAGAFIAHALGL 234
                                       ***************************************************************************** PP

                         TIGR00652 231 tkkkvtvhleggeLeievkedgkvyltGpavlvlegela 269
                                        ++ v+v  +gge+     e g+v+l G+av+v++ge++
  lcl|FitnessBrowser__Miya:8499796 235 AESTVNVRSSGGEILGISIEGGSVFLSGKAVRVFSGEMF 273
                                       ************87766666778*************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (270 nodes)
Target sequences:                          1  (282 residues searched)
Passed MSV filter:                         1  (1); expected 0.0 (0.02)
Passed bias filter:                        1  (1); expected 0.0 (0.02)
Passed Vit filter:                         1  (1); expected 0.0 (0.001)
Passed Fwd filter:                         1  (1); expected 0.0 (1e-05)
Initial search space (Z):                  1  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 8.08
//
[ok]

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code, or see changes to Amino acid biosynthesis since the publication.

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory